Bump pymatgen from 2025.4.20 to 2025.5.1

[dependabot]

Bumps pymatgen from 2025.4.20 to 2025.5.1.

Release notes

Sourced from pymatgen's releases.

v2025.5.1

• lxml is now used for faster Vasprun parsing.
• Minor bug fix for MPRester.get_entries summary_data for larger queries.
• New JSON for ptable with better value/unit handling (also slightly faster) (@​DanielYang59)
• Handle missing trailing newline in ICOHPLIST.lobster (@​alibh95)
• Updated MVLSlabSet with MPSurfaceSet parameters from atomate1 (@​abhardwaj73)

v2025.4.24

• Structure now has a calc_property method that enables one to get a wide range of elasticity, EOS, and phonon properties using matcalc. Requires matcalc to be installed.
• Bug fix and expansion of pymatgen.ext.matproj.MPRester. Now property_data is always consistent with the returned entry in get_entries. Summary data, which is not always consistent but is more comprehensive, can be obtained via a summary_data kwarg.
• PR #4378 Avoid merging if a structure has only one site by @​kmu This PR fixes an error that occurs when calling merge_sites on a structure with only one site. For example:
• PR #4372 Reapply update to ptable vdw radii CSV source and JSON with CRC handbook by @​DanielYang59
  • Update ptable vdw radii CSV source, to fix #4370
  • Revert #4345 and apply changes to CSV vdw radii data source:

  John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL. If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.

Changelog

Sourced from pymatgen's changelog.

v2025.5.1

• lxml is now used for faster Vasprun parsing.
• Minor bug fix for MPRester.get_entries summary_data for larger queries.
• New JSON for ptable with better value/unit handling (also slightly faster) (@​DanielYang59)
• Handle missing trailing newline in ICOHPLIST.lobster (@​alibh95)
• Updated MVLSlabSet with MPSurfaceSet parameters from atomate1 (@​abhardwaj73)

v2025.4.24

• Structure now has a calc_property method that enables one to get a wide range of elasticity, EOS, and phonon properties using matcalc. Requires matcalc to be installed.
• Bug fix and expansion of pymatgen.ext.matproj.MPRester. Now property_data is always consistent with the returned entry in get_entries. Summary data, which is not always consistent but is more comprehensive, can be obtained via a summary_data kwarg.
• PR #4378 Avoid merging if a structure has only one site by @​kmu This PR fixes an error that occurs when calling merge_sites on a structure with only one site. For example:
• PR #4372 Reapply update to ptable vdw radii CSV source and JSON with CRC handbook by @​DanielYang59
  • Update ptable vdw radii CSV source, to fix #4370
  • Revert #4345 and apply changes to CSV vdw radii data source:

  John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL. If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.

Commits

• 0704037 Update docs
• ed69e59 Updated vasp input sets with MPSurfaceSet from atomate1 (#4287)
• 45e8bd4 fix(outputs.py): handle missing trailing newline in ICOHPLIST.lobster (#4350)
• 9dfe704 Use new JSON for ptable with better value/unit handling (also slightly faster...
• 160d699 Merge branch 'master' of github.com:materialsproject/pymatgen
• 191e6bb Add lxml for faster Vasprun parsing.
• 1e36ee5 Moretyping fixes.
• b01797f Fix test regression again.
• c85caf2 Fix test regression.
• 0e07b6b More memory efficient and speedier chunking.
• Additional commits viewable in compare view

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Superseded by #428.